Clay Quartermain was a member of the U.S. Air Force and later he worked with S.H.I.E.L.D.'s storied executive director, Nick Fury. Clay was assigned on a mission to rescue Glenn Talbot from his Russia. After this, he became part of the "Hulkbusters" operation, which attempted to capture the Hulk. After a botched mission in Middletown, AZ Agent Quartermain was wanted by the government but the media attention made him a hero and Fury told him no charges would be brought against him.
Later he was seemingly killed by a self-aware, renegade "Deltan" variety of S.H.I.E.L.D.'s "Life Model Decoys", and replaced by one such LMD. The most advanced of the Deltite LMDs, it rebelled upon learning it was not human, and after several confrontations, perished. The real Quartermain was later found alive in cold storage in S.H.I.E.L.D. HQ, brainwashed by a Hydra.
After he was deprogrammed he dated Jessica Jones in ALIAS. Clay used Jones to bring down a conspiracy against the POTUS. He allowed her to travel to The Raft to confront the Purple Man (Zebediah Killgrave). Quartermain contacted her when he learned Killgrave escaped an hour after she left The Raft. Clay told Jessica that S.H.I.E.L.D. is tracing her phone in order to pick her up, but Jessica insists that she will only come in after Killgrave has been captured.

He was involved in the interrogation of Diamondback that lead to Fury's unsanctioned "Secret War". When Jessica Jones was investigating Hydra due to an attack on Luke Cage, operatives led by Clay stormed the building and killed the Hydra agents. Jessica asks him about the "Secret War," but Clay declines to answer.